PyRadiomics toolbox in Python¶

I) Download the zip file if it does not exist

Extract features¶

First Order Statistics

Shape-based (3D)

Shape-based (2D)

Gray Level Cooccurence Matrix (GLCM)

Gray Level Run Length Matrix (GLRLM)

Gray Level Size Zone Matrix (GLSZM)

Neigbouring Gray Tone Difference Matrix (NGTDM)

In [1]:
import os, zipfile                  #create, read, write, append, and list a ZIP file
import pandas as pd                 #data analysis tools
import seaborn as sns               #statistical data visualization
from six.moves import urllib        #Copy a network object denoted by a URL to a local file
from matplotlib import pyplot as plt

url = "http://www.spl.harvard.edu/publications/bitstream/download/5270"
filename = 'example_data/Tumorbase.zip'
if not os.path.isfile(filename):
    if not os.path.isdir('example_data'):
        os.mkdir('example_data')
    print ("retrieving")
    urllib.request.urlretrieve(url, filename)
else:
    print ("file already downloaded")
    
extracted_path = 'example_data/tumorbase'
if not os.path.isdir(extracted_path):
    print ("unzipping")
    z = zipfile.ZipFile(filename)
    z.extractall('example_data')
    print ("done unzipping")
file already downloaded

1) Setting up data

In [2]:
import os
import SimpleITK as sitk

# Radiomics package
from radiomics import featureextractor

import six, numpy as np

from radiomics import getTestCase

imagepath_1, labelpath_1 = getTestCase('brain1')
imagepath_2, labelpath_2 = getTestCase('brain2')

image_1 = sitk.ReadImage(imagepath_1)
label_1 = sitk.ReadImage(labelpath_1)
image_2 = sitk.ReadImage(imagepath_2)
label_2 = sitk.ReadImage(labelpath_2)

imagepath_1
Out[2]:
'/tmp/pyradiomics/data/brain1_image.nrrd'

2) Show the images

In [3]:
%matplotlib inline
import matplotlib.pyplot as plt

plt.figure(figsize=(20,20))
# First image
plt.subplot(2,2,1)
plt.imshow(sitk.GetArrayFromImage(image_1)[12,:,:], cmap="gray")
plt.title("Brain #1")
plt.subplot(2,2,2)
plt.imshow(sitk.GetArrayFromImage(label_1)[12,:,:])        
plt.title("Segmentation #1")

# Second image
plt.subplot(2,2,3)
plt.imshow(sitk.GetArrayFromImage(image_2)[8,:,:], cmap="gray")        
plt.title("Brain #2")

plt.subplot(2,2,4)
plt.imshow(sitk.GetArrayFromImage(label_2)[8,:,:])        
plt.title("Segmentation #2")

plt.show()

3) Extract the features

In [4]:
import os
# Instantiate the extractor
params = os.path.join(os.getcwd(), '..', 'examples', 'exampleSettings', 'Params.yaml')

extractor = featureextractor.RadiomicsFeaturesExtractor(params)
result_1 = extractor.execute(image_1, label_1)
result_2 = extractor.execute(image_2, label_2)
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
In [36]:
resk=list(result_2.keys())
resv=list(result_2.values())
df=pd.DataFrame([resk,resv]).transpose()
df.columns=['Features','Values']
df
Out[36]:
Features Values
0 diagnostics_Versions_PyRadiomics 2.1.2
1 diagnostics_Versions_Numpy 1.16.2
2 diagnostics_Versions_SimpleITK 1.2.0
3 diagnostics_Versions_PyWavelet 1.0.0
4 diagnostics_Versions_Python 3.6.8
5 diagnostics_Configuration_Settings {'minimumROIDimensions': 2, 'minimumROISize': ...
6 diagnostics_Configuration_EnabledImageTypes {'Original': {}}
7 diagnostics_Image-original_Hash f2b8fbc4d5d1da08a1a70e79a301f8a830139438
8 diagnostics_Image-original_Spacing (0.7812499999999999, 0.7812499999999999, 6.499...
9 diagnostics_Image-original_Size (256, 256, 23)
10 diagnostics_Image-original_Mean 236.202
11 diagnostics_Image-original_Minimum 0
12 diagnostics_Image-original_Maximum 1523
13 diagnostics_Mask-original_Hash b41049c71633e194bee4891750392b72eabd8800
14 diagnostics_Mask-original_Spacing (0.7812499999999999, 0.7812499999999999, 6.499...
15 diagnostics_Mask-original_Size (256, 256, 23)
16 diagnostics_Mask-original_BoundingBox (205, 155, 8, 20, 15, 3)
17 diagnostics_Mask-original_VoxelNum 453
18 diagnostics_Mask-original_VolumeNum 1
19 diagnostics_Mask-original_CenterOfMassIndex (215.21192052980132, 161.45474613686534, 8.589...
20 diagnostics_Mask-original_CenterOfMass (58.134312913907266, -22.717773471183904, -6.8...
21 original_shape_Elongation 0.740769
22 original_shape_Flatness 0.618816
23 original_shape_LeastAxisLength 11.1802
24 original_shape_MajorAxisLength 18.0672
25 original_shape_Maximum2DDiameterColumn 23.5933
26 original_shape_Maximum2DDiameterRow 20.7289
27 original_shape_Maximum2DDiameterSlice 16.313
28 original_shape_Maximum3DDiameter 24.4445
29 original_shape_MeshVolume 1736.02
... ... ...
98 original_glrlm_LowGrayLevelRunEmphasis 0.0076064
99 original_glrlm_RunEntropy 4.20976
100 original_glrlm_RunLengthNonUniformity 365.075
101 original_glrlm_RunLengthNonUniformityNormalized 0.866363
102 original_glrlm_RunPercentage 0.918152
103 original_glrlm_RunVariance 0.150366
104 original_glrlm_ShortRunEmphasis 0.940657
105 original_glrlm_ShortRunHighGrayLevelEmphasis 266.862
106 original_glrlm_ShortRunLowGrayLevelEmphasis 0.00732226
107 original_glszm_GrayLevelNonUniformity 9.63804
108 original_glszm_GrayLevelNonUniformityNormalized 0.0591291
109 original_glszm_GrayLevelVariance 27.8504
110 original_glszm_HighGrayLevelZoneEmphasis 319.988
111 original_glszm_LargeAreaEmphasis 35.3681
112 original_glszm_LargeAreaHighGrayLevelEmphasis 7639.02
113 original_glszm_LargeAreaLowGrayLevelEmphasis 0.184659
114 original_glszm_LowGrayLevelZoneEmphasis 0.0117436
115 original_glszm_SizeZoneNonUniformity 69.184
116 original_glszm_SizeZoneNonUniformityNormalized 0.424442
117 original_glszm_SmallAreaEmphasis 0.677063
118 original_glszm_SmallAreaHighGrayLevelEmphasis 218.879
119 original_glszm_SmallAreaLowGrayLevelEmphasis 0.00988395
120 original_glszm_ZoneEntropy 5.67111
121 original_glszm_ZonePercentage 0.359823
122 original_glszm_ZoneVariance 27.6445
123 original_ngtdm_Busyness 0.151645
124 original_ngtdm_Coarseness 0.0128616
125 original_ngtdm_Complexity 762.182
126 original_ngtdm_Contrast 0.121837
127 original_ngtdm_Strength 3.96631

128 rows × 2 columns

4) Prepare for plotting

In [37]:
feature_1 = np.array([])
feature_2 = np.array([])

for key, value in six.iteritems(result_1):
    print(key)
    if key.startswith("original_"):
        feature_1 = np.append ( feature_1, result_1[key])
        feature_2 = np.append ( feature_2, result_2[key])

result_1['original_glszm_ZoneVariance']
diagnostics_Versions_PyRadiomics
diagnostics_Versions_Numpy
diagnostics_Versions_SimpleITK
diagnostics_Versions_PyWavelet
diagnostics_Versions_Python
diagnostics_Configuration_Settings
diagnostics_Configuration_EnabledImageTypes
diagnostics_Image-original_Hash
diagnostics_Image-original_Spacing
diagnostics_Image-original_Size
diagnostics_Image-original_Mean
diagnostics_Image-original_Minimum
diagnostics_Image-original_Maximum
diagnostics_Mask-original_Hash
diagnostics_Mask-original_Spacing
diagnostics_Mask-original_Size
diagnostics_Mask-original_BoundingBox
diagnostics_Mask-original_VoxelNum
diagnostics_Mask-original_VolumeNum
diagnostics_Mask-original_CenterOfMassIndex
diagnostics_Mask-original_CenterOfMass
original_shape_Elongation
original_shape_Flatness
original_shape_LeastAxisLength
original_shape_MajorAxisLength
original_shape_Maximum2DDiameterColumn
original_shape_Maximum2DDiameterRow
original_shape_Maximum2DDiameterSlice
original_shape_Maximum3DDiameter
original_shape_MeshVolume
original_shape_MinorAxisLength
original_shape_Sphericity
original_shape_SurfaceArea
original_shape_SurfaceVolumeRatio
original_shape_VoxelVolume
original_firstorder_10Percentile
original_firstorder_90Percentile
original_firstorder_Energy
original_firstorder_Entropy
original_firstorder_InterquartileRange
original_firstorder_Kurtosis
original_firstorder_Maximum
original_firstorder_MeanAbsoluteDeviation
original_firstorder_Mean
original_firstorder_Median
original_firstorder_Minimum
original_firstorder_Range
original_firstorder_RobustMeanAbsoluteDeviation
original_firstorder_RootMeanSquared
original_firstorder_Skewness
original_firstorder_TotalEnergy
original_firstorder_Uniformity
original_firstorder_Variance
original_glcm_Autocorrelation
original_glcm_ClusterProminence
original_glcm_ClusterShade
original_glcm_ClusterTendency
original_glcm_Contrast
original_glcm_Correlation
original_glcm_DifferenceAverage
original_glcm_DifferenceEntropy
original_glcm_DifferenceVariance
original_glcm_Id
original_glcm_Idm
original_glcm_Idmn
original_glcm_Idn
original_glcm_Imc1
original_glcm_Imc2
original_glcm_InverseVariance
original_glcm_JointAverage
original_glcm_JointEnergy
original_glcm_JointEntropy
original_glcm_MCC
original_glcm_MaximumProbability
original_glcm_SumAverage
original_glcm_SumEntropy
original_glcm_SumSquares
original_gldm_DependenceEntropy
original_gldm_DependenceNonUniformity
original_gldm_DependenceNonUniformityNormalized
original_gldm_DependenceVariance
original_gldm_GrayLevelNonUniformity
original_gldm_GrayLevelVariance
original_gldm_HighGrayLevelEmphasis
original_gldm_LargeDependenceEmphasis
original_gldm_LargeDependenceHighGrayLevelEmphasis
original_gldm_LargeDependenceLowGrayLevelEmphasis
original_gldm_LowGrayLevelEmphasis
original_gldm_SmallDependenceEmphasis
original_gldm_SmallDependenceHighGrayLevelEmphasis
original_gldm_SmallDependenceLowGrayLevelEmphasis
original_glrlm_GrayLevelNonUniformity
original_glrlm_GrayLevelNonUniformityNormalized
original_glrlm_GrayLevelVariance
original_glrlm_HighGrayLevelRunEmphasis
original_glrlm_LongRunEmphasis
original_glrlm_LongRunHighGrayLevelEmphasis
original_glrlm_LongRunLowGrayLevelEmphasis
original_glrlm_LowGrayLevelRunEmphasis
original_glrlm_RunEntropy
original_glrlm_RunLengthNonUniformity
original_glrlm_RunLengthNonUniformityNormalized
original_glrlm_RunPercentage
original_glrlm_RunVariance
original_glrlm_ShortRunEmphasis
original_glrlm_ShortRunHighGrayLevelEmphasis
original_glrlm_ShortRunLowGrayLevelEmphasis
original_glszm_GrayLevelNonUniformity
original_glszm_GrayLevelNonUniformityNormalized
original_glszm_GrayLevelVariance
original_glszm_HighGrayLevelZoneEmphasis
original_glszm_LargeAreaEmphasis
original_glszm_LargeAreaHighGrayLevelEmphasis
original_glszm_LargeAreaLowGrayLevelEmphasis
original_glszm_LowGrayLevelZoneEmphasis
original_glszm_SizeZoneNonUniformity
original_glszm_SizeZoneNonUniformityNormalized
original_glszm_SmallAreaEmphasis
original_glszm_SmallAreaHighGrayLevelEmphasis
original_glszm_SmallAreaLowGrayLevelEmphasis
original_glszm_ZoneEntropy
original_glszm_ZonePercentage
original_glszm_ZoneVariance
original_ngtdm_Busyness
original_ngtdm_Coarseness
original_ngtdm_Complexity
original_ngtdm_Contrast
original_ngtdm_Strength
Out[37]:
8.721239097486347
In [43]:
feature_2[:3]
len(feature_1)
Out[43]:
107

5) Plot

In [39]:
plt.figure(figsize=(20,20))
plt.subplot(3,1,1)
plt.plot(feature_1)
plt.yscale('log')
plt.title ( "Features from brain #1")
        
plt.subplot(3,1,2)
plt.plot(feature_2)
plt.yscale('log')
plt.title ( "Features from brain #1")

plt.subplot(3,1,3)
plt.plot(feature_1 - feature_2)
plt.yscale('log')
plt.title ( "Difference")
plt.show()

6) Make a numpy array of all the values and correlation

In [44]:
feature_names1 = list(sorted(filter ( lambda k: k.startswith("original_"), result_1 )))
feature_names2 = list(sorted(filter ( lambda k: k.startswith("original_"), result_2 )))
display(feature_names1[:10])

import numpy as np
feature_values1=[]
feature_values2=[]
samples = np.zeros((10,len(feature_names1)))
for feature_name in feature_names1:
     feature_values1 = np.append(feature_values1, result_1[feature_name])
     feature_values2 = np.append(feature_values2, result_2[feature_name])

    
import pandas as pd
result=pd.DataFrame([feature_values1,feature_values2])
result.columns=feature_names1
result
['original_firstorder_10Percentile',
 'original_firstorder_90Percentile',
 'original_firstorder_Energy',
 'original_firstorder_Entropy',
 'original_firstorder_InterquartileRange',
 'original_firstorder_Kurtosis',
 'original_firstorder_Maximum',
 'original_firstorder_Mean',
 'original_firstorder_MeanAbsoluteDeviation',
 'original_firstorder_Median']
Out[44]:
original_firstorder_10Percentile original_firstorder_90Percentile original_firstorder_Energy original_firstorder_Entropy original_firstorder_InterquartileRange original_firstorder_Kurtosis original_firstorder_Maximum original_firstorder_Mean original_firstorder_MeanAbsoluteDeviation original_firstorder_Median ... original_shape_Maximum2DDiameterColumn original_shape_Maximum2DDiameterRow original_shape_Maximum2DDiameterSlice original_shape_Maximum3DDiameter original_shape_MeshVolume original_shape_MinorAxisLength original_shape_Sphericity original_shape_SurfaceArea original_shape_SurfaceVolumeRatio original_shape_VoxelVolume
0 632.0 1044.4 2.918821e+09 4.601936 253.0 2.180773 1266.0 825.235436 133.447262 812.0 ... 49.490855 65.889060 53.593978 69.600990 16147.511800 34.849702 0.479823 6438.821604 0.398750 16412.658691
1 305.2 532.6 7.390377e+07 3.820600 97.0 4.674716 729.0 390.785872 73.554269 375.0 ... 23.593253 20.728928 16.312979 24.444532 1736.017863 13.383590 0.751304 929.760151 0.535571 1797.180176

2 rows × 107 columns

In [45]:
import seaborn as sns

# Construct a pandas dataframe from the samples
#d = pd.DataFrame(data=samples, columns=feature_names)
corr = result.corr()

# Set up the matplotlib figure, make it big!
f, ax = plt.subplots(figsize=(15, 10))

# Draw the heatmap using seaborn
sns.heatmap(corr, vmax=.8, square=True)
plt.show()

II) Extract features

First Order Statistics

Shape-based (3D)

Shape-based (2D)

Gray Level Cooccurence Matrix (GLCM)

Gray Level Run Length Matrix (GLRLM)

Gray Level Size Zone Matrix (GLSZM)

Neigbouring Gray Tone Difference Matrix (NGTDM)

In [46]:
import SimpleITK as sitk
from radiomics import featureextractor
# Load up the segmentations, 1 to 10 and extract the features

params = os.path.join(os.getcwd(), '..', 'examples', 'exampleSettings', 'Params.yaml')
extractor = featureextractor.RadiomicsFeaturesExtractor(params)

# hang on to all our features
features = {}

for case_id in range(1,11):
    path = 'example_data/tumorbase/AutomatedSegmentation/case{}/'.format(case_id)
    image = sitk.ReadImage(path + "grayscale.nrrd")
    mask = sitk.ReadImage(path + "segmented.nrrd")
    # Tumor is in label value 6
    features[case_id] = extractor.execute ( image, mask, label=6 )
# A list of the valid features, sorted
feature_names = list(sorted(filter ( lambda k: k.startswith("original_"), features[1] )))
feature_names[:10]
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
Out[46]:
['original_firstorder_10Percentile',
 'original_firstorder_90Percentile',
 'original_firstorder_Energy',
 'original_firstorder_Entropy',
 'original_firstorder_InterquartileRange',
 'original_firstorder_Kurtosis',
 'original_firstorder_Maximum',
 'original_firstorder_Mean',
 'original_firstorder_MeanAbsoluteDeviation',
 'original_firstorder_Median']
In [47]:
features
Out[47]:
{1: OrderedDict([('diagnostics_Versions_PyRadiomics', '2.1.2'),
              ('diagnostics_Versions_Numpy', '1.16.2'),
              ('diagnostics_Versions_SimpleITK', '1.2.0'),
              ('diagnostics_Versions_PyWavelet', '1.0.0'),
              ('diagnostics_Versions_Python', '3.6.8'),
              ('diagnostics_Configuration_Settings',
               {'minimumROIDimensions': 2,
                'minimumROISize': None,
                'normalize': False,
                'normalizeScale': 1,
                'removeOutliers': None,
                'resampledPixelSpacing': None,
                'interpolator': 'sitkBSpline',
                'preCrop': False,
                'padDistance': 5,
                'distances': [1],
                'force2D': False,
                'force2Ddimension': 0,
                'resegmentRange': None,
                'label': 6,
                'additionalInfo': True}),
              ('diagnostics_Configuration_EnabledImageTypes',
               {'Original': {}}),
              ('diagnostics_Image-original_Hash',
               '4b422fa3af4c0b3c006422d6cac17821f98ebda2'),
              ('diagnostics_Image-original_Spacing', (0.9375, 0.9375, 1.5)),
              ('diagnostics_Image-original_Size', (256, 256, 123)),
              ('diagnostics_Image-original_Mean', 39.73005862352325),
              ('diagnostics_Image-original_Minimum', 0.0),
              ('diagnostics_Image-original_Maximum', 833.0),
              ('diagnostics_Mask-original_Hash',
               '9d7b71692f7c9fe934523b67d82ebe6f97d1ce86'),
              ('diagnostics_Mask-original_Spacing', (0.9375, 0.9375, 1.5)),
              ('diagnostics_Mask-original_Size', (256, 256, 123)),
              ('diagnostics_Mask-original_BoundingBox',
               (103, 168, 35, 54, 42, 28)),
              ('diagnostics_Mask-original_VoxelNum', 28381),
              ('diagnostics_Mask-original_VolumeNum', 1),
              ('diagnostics_Mask-original_CenterOfMassIndex',
               (129.5908882703217, 189.75744335999437, 49.803706705190095)),
              ('diagnostics_Mask-original_CenterOfMass',
               (17.544439942214865, 1.9604577534265815, 58.36660314999472)),
              ('original_shape_Elongation', 0.794856283000445),
              ('original_shape_Flatness', 0.5829014701298105),
              ('original_shape_LeastAxisLength', 28.585273833005722),
              ('original_shape_MajorAxisLength', 49.03963242130761),
              ('original_shape_Maximum2DDiameterColumn', 51.70242378264292),
              ('original_shape_Maximum2DDiameterRow', 45.621104285736),
              ('original_shape_Maximum2DDiameterSlice', 58.245842126284),
              ('original_shape_Maximum3DDiameter', 58.73540377191596),
              ('original_shape_MeshVolume', 37283.367919921875),
              ('original_shape_MinorAxisLength', 38.979459946108676),
              ('original_shape_Sphericity', 0.6598900382284406),
              ('original_shape_SurfaceArea', 8178.794757930033),
              ('original_shape_SurfaceVolumeRatio', 0.2193684533944639),
              ('original_shape_VoxelVolume', 37416.357421875),
              ('original_firstorder_10Percentile', 140.0),
              ('original_firstorder_90Percentile', 175.0),
              ('original_firstorder_Energy', 703288387.0),
              ('original_firstorder_Entropy', 1.407119095841021),
              ('original_firstorder_InterquartileRange', 18.0),
              ('original_firstorder_Kurtosis', 5.772689236689695),
              ('original_firstorder_Maximum', 291.0),
              ('original_firstorder_MeanAbsoluteDeviation',
               10.982512664874108),
              ('original_firstorder_Mean', 156.77040978119163),
              ('original_firstorder_Median', 155.0),
              ('original_firstorder_Minimum', 66.0),
              ('original_firstorder_Range', 225.0),
              ('original_firstorder_RobustMeanAbsoluteDeviation',
               7.6494640117776225),
              ('original_firstorder_RootMeanSquared', 157.41745118471903),
              ('original_firstorder_Skewness', 0.7568529462163773),
              ('original_firstorder_TotalEnergy', 927186838.3300781),
              ('original_firstorder_Uniformity', 0.43976272587212006),
              ('original_firstorder_Variance', 203.2925545306454),
              ('original_glcm_Autocorrelation', 23.02086232451176),
              ('original_glcm_ClusterProminence', 5.2274395746651035),
              ('original_glcm_ClusterShade', 0.5363520463071897),
              ('original_glcm_ClusterTendency', 1.0646752659349863),
              ('original_glcm_Contrast', 0.6042855954860485),
              ('original_glcm_Correlation', 0.27504610069981744),
              ('original_glcm_DifferenceAverage', 0.5085697614251752),
              ('original_glcm_DifferenceEntropy', 1.1996914930109133),
              ('original_glcm_DifferenceVariance', 0.3430553610135786),
              ('original_glcm_Id', 0.7601740475258996),
              ('original_glcm_Idm', 0.7551027250539343),
              ('original_glcm_Idmn', 0.9940961816677637),
              ('original_glcm_Idn', 0.9544678934763919),
              ('original_glcm_Imc1', -0.051228352724291396),
              ('original_glcm_Imc2', 0.3425366377362223),
              ('original_glcm_InverseVariance', 0.437644226953438),
              ('original_glcm_JointAverage', 4.785995154182346),
              ('original_glcm_JointEnergy', 0.21155483301820516),
              ('original_glcm_JointEntropy', 2.7082121788624534),
              ('original_glcm_MCC', 0.3434195543527093),
              ('original_glcm_MaximumProbability', 0.36680411286664766),
              ('original_glcm_SumAverage', 9.571990308364692),
              ('original_glcm_SumEntropy', 2.0400770221007183),
              ('original_glcm_SumSquares', 0.4172402153552586),
              ('original_gldm_DependenceEntropy', 5.651024217126519),
              ('original_gldm_DependenceNonUniformity', 1325.3549557802755),
              ('original_gldm_DependenceNonUniformityNormalized',
               0.046698670088449155),
              ('original_gldm_DependenceVariance', 33.861326489794834),
              ('original_gldm_GrayLevelNonUniformity', 12480.905922976639),
              ('original_gldm_GrayLevelVariance', 0.42822779811730444),
              ('original_gldm_HighGrayLevelEmphasis', 23.398329868574045),
              ('original_gldm_LargeDependenceEmphasis', 224.39586342975934),
              ('original_gldm_LargeDependenceHighGrayLevelEmphasis',
               5210.004298650506),
              ('original_gldm_LargeDependenceLowGrayLevelEmphasis',
               10.079057835608813),
              ('original_gldm_LowGrayLevelEmphasis', 0.046066072680411414),
              ('original_gldm_SmallDependenceEmphasis', 0.023471854578384868),
              ('original_gldm_SmallDependenceHighGrayLevelEmphasis',
               0.6209139175643873),
              ('original_gldm_SmallDependenceLowGrayLevelEmphasis',
               0.0011797683485162763),
              ('original_glrlm_GrayLevelNonUniformity', 5361.074859168112),
              ('original_glrlm_GrayLevelNonUniformityNormalized',
               0.37206078398825027),
              ('original_glrlm_GrayLevelVariance', 0.5780095826636417),
              ('original_glrlm_HighGrayLevelRunEmphasis', 23.63648816520193),
              ('original_glrlm_LongRunEmphasis', 6.712932378878997),
              ('original_glrlm_LongRunHighGrayLevelEmphasis',
               157.0801381458293),
              ('original_glrlm_LongRunLowGrayLevelEmphasis',
               0.3016840208223139),
              ('original_glrlm_LowGrayLevelRunEmphasis', 0.046703187080956984),
              ('original_glrlm_RunEntropy', 3.476352318156401),
              ('original_glrlm_RunLengthNonUniformity', 5465.472667273132),
              ('original_glrlm_RunLengthNonUniformityNormalized',
               0.3758276552552058),
              ('original_glrlm_RunPercentage', 0.5075605835973688),
              ('original_glrlm_RunVariance', 2.7168923119446124),
              ('original_glrlm_ShortRunEmphasis', 0.6299285666540271),
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              ('original_firstorder_Kurtosis', 3.4472109600920557),
              ('original_firstorder_Maximum', 274.0),
              ('original_firstorder_MeanAbsoluteDeviation',
               30.368744453201337),
              ('original_firstorder_Mean', 155.30604982206407),
              ('original_firstorder_Median', 161.0),
              ('original_firstorder_Minimum', 0.0),
              ('original_firstorder_Range', 274.0),
              ('original_firstorder_RobustMeanAbsoluteDeviation',
               20.110905091497862),
              ('original_firstorder_RootMeanSquared', 160.18850977555067),
              ('original_firstorder_Skewness', -0.6457338562080939),
              ('original_firstorder_TotalEnergy', 617897176.6113281),
              ('original_firstorder_Uniformity', 0.191563975594573),
              ('original_firstorder_Variance', 1540.389552778246),
              ('original_glcm_Autocorrelation', 48.632122704617245),
              ('original_glcm_ClusterProminence', 185.2458196874492),
              ('original_glcm_ClusterShade', -11.399576939683369),
              ('original_glcm_ClusterTendency', 7.024301912634512),
              ('original_glcm_Contrast', 2.236726817788646),
              ('original_glcm_Correlation', 0.5146242498837945),
              ('original_glcm_DifferenceAverage', 1.040976097311836),
              ('original_glcm_DifferenceEntropy', 1.8952897356976943),
              ('original_glcm_DifferenceVariance', 1.1338027509380604),
              ('original_glcm_Id', 0.6201349639864393),
              ('original_glcm_Idm', 0.5872706578834982),
              ('original_glcm_Idmn', 0.9829595943759244),
              ('original_glcm_Idn', 0.920118770218725),
              ('original_glcm_Imc1', -0.1087204203821225),
              ('original_glcm_Imc2', 0.6323935170223918),
              ('original_glcm_InverseVariance', 0.46677143450049063),
              ('original_glcm_JointAverage', 6.88725030985373),
              ('original_glcm_JointEnergy', 0.05426926900734254),
              ('original_glcm_JointEntropy', 4.896532484640679),
              ('original_glcm_MCC', 0.5242333592383907),
              ('original_glcm_MaximumProbability', 0.1293649359648895),
              ('original_glcm_SumAverage', 13.774500619707457),
              ('original_glcm_SumEntropy', 3.3953503956008433),
              ('original_glcm_SumSquares', 2.3152571826057904),
              ('original_gldm_DependenceEntropy', 6.647010000027693),
              ('original_gldm_DependenceNonUniformity', 1060.801040240898),
              ('original_gldm_DependenceNonUniformityNormalized',
               0.05807834876763744),
              ('original_gldm_DependenceVariance', 24.707817345826257),
              ('original_gldm_GrayLevelNonUniformity', 3498.9160142348755),
              ('original_gldm_GrayLevelVariance', 2.5652030779332375),
              ('original_gldm_HighGrayLevelEmphasis', 47.91305776074459),
              ('original_gldm_LargeDependenceEmphasis', 102.5327675882836),
              ('original_gldm_LargeDependenceHighGrayLevelEmphasis',
               5374.51628798248),
              ('original_gldm_LargeDependenceLowGrayLevelEmphasis',
               2.248120000472389),
              ('original_gldm_LowGrayLevelEmphasis', 0.030438485150673763),
              ('original_gldm_SmallDependenceEmphasis', 0.0646620920782374),
              ('original_gldm_SmallDependenceHighGrayLevelEmphasis',
               2.3299230947114626),
              ('original_gldm_SmallDependenceLowGrayLevelEmphasis',
               0.003986952282326335),
              ('original_glrlm_GrayLevelNonUniformity', 2193.0277923537597),
              ('original_glrlm_GrayLevelNonUniformityNormalized',
               0.17166911757014824),
              ('original_glrlm_GrayLevelVariance', 2.9248685250164614),
              ('original_glrlm_HighGrayLevelRunEmphasis', 46.32680575357054),
              ('original_glrlm_LongRunEmphasis', 2.911404449837207),
              ('original_glrlm_LongRunHighGrayLevelEmphasis',
               145.24488707537813),
              ('original_glrlm_LongRunLowGrayLevelEmphasis',
               0.07718833661659365),
              ('original_glrlm_LowGrayLevelRunEmphasis', 0.033396225375294526),
              ('original_glrlm_RunEntropy', 3.982463148227209),
              ('original_glrlm_RunLengthNonUniformity', 7292.755184279124),
              ('original_glrlm_RunLengthNonUniformityNormalized',
               0.5673349236147036),
              ('original_glrlm_RunPercentage', 0.6991598054286255),
              ('original_glrlm_RunVariance', 0.8312168075619124),
              ('original_glrlm_ShortRunEmphasis', 0.7803088193148869),
              ('original_glrlm_ShortRunHighGrayLevelEmphasis',
               35.092554893986055),
              ('original_glrlm_ShortRunLowGrayLevelEmphasis',
               0.027968201854090553),
              ('original_glszm_GrayLevelNonUniformity', 141.59959349593495),
              ('original_glszm_GrayLevelNonUniformityNormalized',
               0.143902025910503),
              ('original_glszm_GrayLevelVariance', 5.280511558926566),
              ('original_glszm_HighGrayLevelZoneEmphasis', 31.442073170731707),
              ('original_glszm_LargeAreaEmphasis', 56852.05386178862),
              ('original_glszm_LargeAreaHighGrayLevelEmphasis',
               2931447.1788617885),
              ('original_glszm_LargeAreaLowGrayLevelEmphasis',
               1156.8921826083727),
              ('original_glszm_LowGrayLevelZoneEmphasis', 0.07838788722751112),
              ('original_glszm_SizeZoneNonUniformity', 290.7743902439024),
              ('original_glszm_SizeZoneNonUniformityNormalized',
               0.29550242910965696),
              ('original_glszm_SmallAreaEmphasis', 0.5604644690421469),
              ('original_glszm_SmallAreaHighGrayLevelEmphasis',
               17.61193874232189),
              ('original_glszm_SmallAreaLowGrayLevelEmphasis',
               0.0474083490072353),
              ('original_glszm_ZoneEntropy', 5.485732273732717),
              ('original_glszm_ZonePercentage', 0.05387352860662469),
              ('original_glszm_ZoneVariance', 56507.5063196097),
              ('original_ngtdm_Busyness', 23.245251276221417),
              ('original_ngtdm_Coarseness', 0.0004825537269538527),
              ('original_ngtdm_Complexity', 37.85597455257226),
              ('original_ngtdm_Contrast', 0.035694284374923474),
              ('original_ngtdm_Strength', 0.020623856827336924)]),
 10: OrderedDict([('diagnostics_Versions_PyRadiomics', '2.1.2'),
              ('diagnostics_Versions_Numpy', '1.16.2'),
              ('diagnostics_Versions_SimpleITK', '1.2.0'),
              ('diagnostics_Versions_PyWavelet', '1.0.0'),
              ('diagnostics_Versions_Python', '3.6.8'),
              ('diagnostics_Configuration_Settings',
               {'minimumROIDimensions': 2,
                'minimumROISize': None,
                'normalize': False,
                'normalizeScale': 1,
                'removeOutliers': None,
                'resampledPixelSpacing': None,
                'interpolator': 'sitkBSpline',
                'preCrop': False,
                'padDistance': 5,
                'distances': [1],
                'force2D': False,
                'force2Ddimension': 0,
                'resegmentRange': None,
                'label': 6,
                'additionalInfo': True}),
              ('diagnostics_Configuration_EnabledImageTypes',
               {'Original': {}}),
              ('diagnostics_Image-original_Hash',
               '35f1580c86e11e0a4463c760b1a1f771982fa496'),
              ('diagnostics_Image-original_Spacing', (0.9375, 0.9375, 1.5)),
              ('diagnostics_Image-original_Size', (256, 256, 123)),
              ('diagnostics_Image-original_Mean', 38.50025729047574),
              ('diagnostics_Image-original_Minimum', 0.0),
              ('diagnostics_Image-original_Maximum', 792.0),
              ('diagnostics_Mask-original_Hash',
               'f89deb69860d0c151f57f8797191e449c15ee27b'),
              ('diagnostics_Mask-original_Spacing', (0.9375, 0.9375, 1.5)),
              ('diagnostics_Mask-original_Size', (256, 256, 123)),
              ('diagnostics_Mask-original_BoundingBox',
               (105, 86, 22, 75, 55, 30)),
              ('diagnostics_Mask-original_VoxelNum', 33502),
              ('diagnostics_Mask-original_VolumeNum', 1),
              ('diagnostics_Mask-original_CenterOfMassIndex',
               (143.44071995701748, 111.29457942809384, 38.03799773147872)),
              ('diagnostics_Mask-original_CenterOfMass',
               (35.193003402781926, 14.944674959703889, -15.192331786162029)),
              ('original_shape_Elongation', 0.5825062842587055),
              ('original_shape_Flatness', 0.4507379954185646),
              ('original_shape_LeastAxisLength', 28.938898690625127),
              ('original_shape_MajorAxisLength', 64.20337088235011),
              ('original_shape_Maximum2DDiameterColumn', 68.58528563948684),
              ('original_shape_Maximum2DDiameterRow', 49.50142043416532),
              ('original_shape_Maximum2DDiameterSlice', 71.2746667828058),
              ('original_shape_Maximum3DDiameter', 75.79848386511435),
              ('original_shape_MeshVolume', 44058.251953125),
              ('original_shape_MinorAxisLength', 37.398867009561336),
              ('original_shape_Sphericity', 0.5456363057624773),
              ('original_shape_SurfaceArea', 11056.025695975895),
              ('original_shape_SurfaceVolumeRatio', 0.25094108835136625),
              ('original_shape_VoxelVolume', 44167.67578125),
              ('original_firstorder_10Percentile', 48.0),
              ('original_firstorder_90Percentile', 81.0),
              ('original_firstorder_Energy', 143734129.0),
              ('original_firstorder_Entropy', 1.340339712993897),
              ('original_firstorder_InterquartileRange', 17.0),
              ('original_firstorder_Kurtosis', 6.272806104662042),
              ('original_firstorder_Maximum', 252.0),
              ('original_firstorder_MeanAbsoluteDeviation',
               10.760356983847393),
              ('original_firstorder_Mean', 63.95101784968062),
              ('original_firstorder_Median', 63.0),
              ('original_firstorder_Minimum', 0.0),
              ('original_firstorder_Range', 252.0),
              ('original_firstorder_RobustMeanAbsoluteDeviation',
               7.211091998282539),
              ('original_firstorder_RootMeanSquared', 65.50049524029401),
              ('original_firstorder_Skewness', 0.49756071259781126),
              ('original_firstorder_TotalEnergy', 189493236.47460938),
              ('original_firstorder_Uniformity', 0.4995326982582334),
              ('original_firstorder_Variance', 200.58219271360892),
              ('original_glcm_Autocorrelation', 9.328989598930708),
              ('original_glcm_ClusterProminence', 3.7629784821130325),
              ('original_glcm_ClusterShade', 0.18939743667708436),
              ('original_glcm_ClusterTendency', 0.9122758953194448),
              ('original_glcm_Contrast', 0.433299681559846),
              ('original_glcm_Correlation', 0.3543879611134286),
              ('original_glcm_DifferenceAverage', 0.3824281995386356),
              ('original_glcm_DifferenceEntropy', 1.0588296124536536),
              ('original_glcm_DifferenceVariance', 0.2847943492494132),
              ('original_glcm_Id', 0.816503174342922),
              ('original_glcm_Idm', 0.8137608790919745),
              ('original_glcm_Idmn', 0.9964788013733197),
              ('original_glcm_Idn', 0.9684469827398222),
              ('original_glcm_Imc1', -0.09185235861809793),
              ('original_glcm_Imc2', 0.4315021657555729),
              ('original_glcm_InverseVariance', 0.3443315038368407),
              ('original_glcm_JointAverage', 3.0346597601429717),
              ('original_glcm_JointEnergy', 0.3152003621809232),
              ('original_glcm_JointEntropy', 2.384611209692664),
              ('original_glcm_MCC', 0.3731486518544802),
              ('original_glcm_MaximumProbability', 0.5299275567588405),
              ('original_glcm_SumAverage', 6.069319520285941),
              ('original_glcm_SumEntropy', 1.898465524023218),
              ('original_glcm_SumSquares', 0.3363938942198226),
              ('original_gldm_DependenceEntropy', 5.49398634173834),
              ('original_gldm_DependenceNonUniformity', 1404.051041728852),
              ('original_gldm_DependenceNonUniformityNormalized',
               0.041909469337020236),
              ('original_gldm_DependenceVariance', 49.757052774248194),
              ('original_gldm_GrayLevelNonUniformity', 16735.34445704734),
              ('original_gldm_GrayLevelVariance', 0.38663444904191635),
              ('original_gldm_HighGrayLevelEmphasis', 9.88164885678467),
              ('original_gldm_LargeDependenceEmphasis', 310.1542594471972),
              ('original_gldm_LargeDependenceHighGrayLevelEmphasis',
               2834.444242134798),
              ('original_gldm_LargeDependenceLowGrayLevelEmphasis',
               35.94942035132654),
              ('original_gldm_LowGrayLevelEmphasis', 0.12220355166615725),
              ('original_gldm_SmallDependenceEmphasis', 0.02007727369335469),
              ('original_gldm_SmallDependenceHighGrayLevelEmphasis',
               0.275158415569856),
              ('original_gldm_SmallDependenceLowGrayLevelEmphasis',
               0.0030507609365585425),
              ('original_glrlm_GrayLevelNonUniformity', 4770.358532796219),
              ('original_glrlm_GrayLevelNonUniformityNormalized',
               0.340363608382969),
              ('original_glrlm_GrayLevelVariance', 0.662228609242522),
              ('original_glrlm_HighGrayLevelRunEmphasis', 10.702721366789941),
              ('original_glrlm_LongRunEmphasis', 12.557228953336582),
              ('original_glrlm_LongRunHighGrayLevelEmphasis',
               116.87335887791674),
              ('original_glrlm_LongRunLowGrayLevelEmphasis',
               1.4541482477567451),
              ('original_glrlm_LowGrayLevelRunEmphasis', 0.12854891070459382),
              ('original_glrlm_RunEntropy', 3.7927797235122473),
              ('original_glrlm_RunLengthNonUniformity', 4767.087809116933),
              ('original_glrlm_RunLengthNonUniformityNormalized',
               0.33498316598211225),
              ('original_glrlm_RunPercentage', 0.41781432107382793),
              ('original_glrlm_RunVariance', 6.453790920101132),
              ('original_glrlm_ShortRunEmphasis', 0.5940185742277792),
              ('original_glrlm_ShortRunHighGrayLevelEmphasis',
               6.8231279946783445),
              ('original_glrlm_ShortRunLowGrayLevelEmphasis',
               0.07868870925795055),
              ('original_glszm_GrayLevelNonUniformity', 120.9375),
              ('original_glszm_GrayLevelNonUniformityNormalized',
               0.2699497767857143),
              ('original_glszm_GrayLevelVariance', 2.4907475685586733),
              ('original_glszm_HighGrayLevelZoneEmphasis', 15.229910714285714),
              ('original_glszm_LargeAreaEmphasis', 1224494.138392857),
              ('original_glszm_LargeAreaHighGrayLevelEmphasis',
               11474672.457589285),
              ('original_glszm_LargeAreaLowGrayLevelEmphasis',
               135031.32683915953),
              ('original_glszm_LowGrayLevelZoneEmphasis', 0.1846119770030755),
              ('original_glszm_SizeZoneNonUniformity', 135.60714285714286),
              ('original_glszm_SizeZoneNonUniformityNormalized',
               0.30269451530612246),
              ('original_glszm_SmallAreaEmphasis', 0.5656454742125366),
              ('original_glszm_SmallAreaHighGrayLevelEmphasis',
               9.20637049344557),
              ('original_glszm_SmallAreaLowGrayLevelEmphasis',
               0.09538076016235757),
              ('original_glszm_ZoneEntropy', 4.486520421879557),
              ('original_glszm_ZonePercentage', 0.013372335979941497),
              ('original_glszm_ZoneVariance', 1218901.9030412945),
              ('original_ngtdm_Busyness', 89.00970507751772),
              ('original_ngtdm_Coarseness', 0.00025931753874922265),
              ('original_ngtdm_Complexity', 19.569720812548336),
              ('original_ngtdm_Contrast', 0.0037167286858861277),
              ('original_ngtdm_Strength', 0.02891704912500508)])}

III) Show images and labels

In [48]:
case_id=2
path = 'example_data/tumorbase/AutomatedSegmentation/case{}/'.format(case_id)
im = sitk.ReadImage(path + "grayscale.nrrd")
mk = sitk.ReadImage(path + "segmented.nrrd")
image=sitk.GetArrayFromImage(im)
mask=sitk.GetArrayFromImage(mk)
print(image.shape)
for i in range(image.shape[0]-1):
    plt.figure(figsize=(8,8))
    plt.subplot(1,2,1)
    plt.title('Image')
    plt.imshow(image[i,:,:], cmap="gray")
    plt.subplot(1,2,2)
    plt.title('Mask')
    plt.imshow(mask[i,:,:], cmap="gray")
(123, 256, 256)
/home/mrclnndrd/anaconda3/envs/pyradiomics/lib/python3.6/site-packages/matplotlib/pyplot.py:514: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)

IV) Make a numpy array of all the values

In [49]:
import numpy as np

samples = np.zeros((10,len(feature_names)))
for case_id in range(1,11):
    a = np.array([])
    for feature_name in feature_names:
        a = np.append(a, features[case_id][feature_name])
    samples[case_id-1,:] = a
    
# May have NaNs
samples = np.nan_to_num(samples)

V) Plot features as a heatmap

In [50]:
import pandas as pd
import seaborn as sns

# Construct a pandas dataframe from the samples
d = pd.DataFrame(data=samples, columns=feature_names)
corr = d.corr()

# Set up the matplotlib figure, make it big!
f, ax = plt.subplots(figsize=(15, 10))

# Draw the heatmap using seaborn
sns.heatmap(corr, vmax=.8, square=True)
plt.show()

VI) Cluster the heatmap

In [51]:
# Choose a subset of features for clustering
dd = d.iloc[:,1:50]

pp = sns.clustermap(dd.corr(), linewidths=.5, figsize=(13,13))
_ = plt.setp(pp.ax_heatmap.get_yticklabels(), rotation=0)

plt.show()
In [52]:
import time
path="/home/mrclnndrd/Dropbox/Projetos/Radiomics/Image/"

for i in range(9):
    print(i)
    time.sleep(1)
    image_1 = sitk.ReadImage(path+"000"+str(i+1)+".dcm")
    im=sitk.GetArrayFromImage(image_1)
    plt.figure(figsize=(8,8))
    plt.imshow(im[0,:,:], cmap="gray")
    
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